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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: derive SEX for each subject of a subject list from the
subject's collected answer.
Input: a subject list naming each subject, and long-form Operational Data Model (ODM) data with one row per collected item.
Variables:
SEXwould be the subject's answer to the sex question.
Each record is built from the subject list, so none of them was built from collected items, and an item has no records of its own to be read from. The request is rejected before any data is read.
How to fix
Build the records from the collected items, one per subject, and read the answer there:
input:
ODM: input/odm.csv
columns:
- name: USUBJID
derivation: ODM.SubjectKey
- name: SEX
derivation: {odm: ODM.IT.DM.SEX}
A subject list that decides which subjects appear is then a filter or a lookup against those records, not the place they are built from.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- validation
- condition
- invalid_odm_context
- rule
- NAME-11
expected/error.yaml
phase: validation
condition: invalid_odm_context
spec_paths:
- columns.SEX.derivation.odm
rule: NAME-11
context:
dataset: ODM
location: column
Inputs
Under review2 source filesinput/dm_raw.csv
Edit2 rows| STUDYID | USUBJID |
|---|---|
| STUDY01 | |
| STUDY01 |
input/odm.csv
Edit4 rows| StudyOID | MetaDataVersionOID | SubjectKey | StudyEventOID | StudyEventRepeatKey | FormOID | FormRepeatKey | ItemGroupOID | ItemGroupRepeatKey | ItemOID | Value |
|---|---|---|---|---|---|---|---|---|---|---|
| STUDY01 | MDV.1 | 001 | SCREENING | 1 | FO.DM | 1 | IG.DM | 1 | IT.DM.SEX | F |
| STUDY01 | MDV.1 | 001 | SCREENING | 1 | FO.DM | 1 | IG.DM | 1 | IT.DM.AGE | 34 |
| STUDY01 | MDV.1 | 002 | SCREENING | 1 | FO.DM | 1 | IG.DM | 1 | IT.DM.SEX | M |
| STUDY01 | MDV.1 | 002 | SCREENING | 1 | FO.DM | 1 | IG.DM | 1 | IT.DM.AGE | 28 |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Human review and assessment
| Variable Name | Variable Label | Type | Length | Controlled Terms or Format | Origin | Core | Conversion Definition | Variable Type | Variable Order | Comments for Define |
|---|---|---|---|---|---|---|---|---|---|---|
| STUDYID | Study Identifier | Char | Collected | Copy value from DM_RAW.STUDYID. | SDTM | 1 | ||||
| USUBJID | Unique Subject Identifier | Char | Collected | Copy value from DM_RAW.USUBJID. | SDTM | 2 | ||||
| SEX | Sex | Char | Collected | Read collected ODM item IT.DM.SEX; no identified record yields blank. | SDTM | 3 |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 1.7 | 2026-10-20 | yamaa docs build | Read a specification in the 1.0 surface as its 0.5 counterpart; state that missing values stay missing where a mapping declares no missing handler, and leave out a declared missing answer that restates a handler's default | ||
| 1.6 | 2026-10-17 | yamaa docs build | Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight | ||
| 1.5 | 2026-10-17 | yamaa docs build | Name collected precision in words instead of letter codes; state imputation fallbacks, minimum source precision, bounds ignored outside the collected period, and invalid text with no handler as an error; describe date and datetime shifts, imputation flag codes, and partial text giving no date part | ||
| 1.4 | 2026-10-15 | yamaa docs build | State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks | ||
| 1.3 | 2026-09-29 | yamaa docs build | Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata | ||
| 1.2 | 2026-09-29 | yamaa docs build | Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived | ||
| 1.1 | 2026-09-29 | yamaa docs build | Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML | ||
| 1.0 | yamaa docs build | Initial generation from spec.yaml |